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Clonal diversity in cancer has been proposed as a mechanism underlying patient-to-patient variability in therapeutic response, as well as the variability in the likelihood and the time to relapse of acute myeloid leukemia (AML) and other cancers. As a neoplasm develops it often continues to mutate, diversifying into differing clonal populations. Darwinian evolutionary pressures such as inherent fitness imbalances, immune system interactions, and chemotherapy treatments target sensitive clones and drive competition between the clonal populations; selecting for dynamic and resistant cell lines. In this way clonal diversity is conceivable as an impediment to a complete remission with more populations offering more opportunities for therapy resistance. Bulk next generation sequencing (NGS) is currently used to assess clonal composition in leukemia but requires several broad assumptions be made, which can result in incorrect assessments of diversity. Factors such as differences in zygosity of mutations, convergent evolution, or contamination with wild-type/non-cancerous cells can artificially raise or lower reported variable allele frequencies (VAF), leading to errors in clonal assessments. To examine discrepancies between the actual clonal structure and the clonal structures determined through bulk sequencing we developed a novel method of sampling the cell population to identify concurrent mutations. We first created an in silico model which randomly draws cell samples from a simulated tumor multiple times and calculates the VAF for each mutant allele in each sample. By tracking the correlation of mutations between sample replicates, a clonal composition that is not observable from the bulk NGS VAF becomes apparent. We then created in vitro model tumors from AML cell lines, isolated low cell number samples via flow cytometry, and applied a multiplex/nested PCR protocol with pyrosequencing to quantify VAFs in each sample. Again, by calculating the correlation of mutant alleles between replicates, previously unseen with NGS characteristics of the clonal structure becomes evident. Population sampling analysis may potentially offer a solution for clarifying how we can interpret NGS clonal analyses.

Langerhan’s cells (LCs) are the immune sentinels of the skin, sampling the cutaneous microenvironment and presenting captured antigen to T cells. A sheet-like proliferation of LCs is termed Langerhan’s cell histiocytosis (LCH), an enigmatic and poorly understood disorder with a widely varied clinical spectrum and disease course. In non-pulmonary LCH all cases reported to date have been monoclonal. Clonality argues for LCH as a neoplastic rather than reactive disorder. After initial investigation of the limitations of formalin fixed paraffin embedded tissues for downstream analysis, lesions of LCH were collected from 4 sites across Scotland. To further define the spectrum of LCH, clonality was assessed using an X inactivation assay based on the polymorphous region of the Human Androgen Receptor. To improve understanding of the assay, a study on post-mortem material was undertaken. This demonstrated a unique insight into patterns of X inactivation across different tissues of the same individual and highlighted potential pitfalls in interpretation. An important question was whether lesions of LCH associated with haematopoietic neoplasms were polyclonal or monoclonal proliferations? For the first time, associations of LCH with B-cutaneous lymphoid hyperplasia (B-CLH), lymphomatoid papulosis (LyP) and mycosis fungoides (MF) are reported. In two female cases, the LCs were polyclonal providing some reassurance that such lesions are reactive in nature and should not be regarded as potential second neoplasms. In a more expanded study a wide variety of primary LCH lesions were assessed for clonality. Significant limitations were posed by the quality of the material available; in 2 cases the lesions were found to be polyclonal. This is the first time such a result has been reported. Monoclonality was identified in 2 other cases including one of pulmonary LCH. The findings reported herein suggest that clonality and hence neoplasia cannot be assumed in all cases of primary non-pulmonary LCH. The possible functions of LCs in cutaneous lymphoma were explored. In T-cell lymphoma 2 cases reported here suggest a role for LCs in disease progression. In contrast, LCs play no significant part in the development or progression of cutaneous B-cell proliferations although other types of dendritic cells probably have an important role. By studying proliferations of LCs in a variety of settings, this work has extended knowledge of the spectrum of LCH. Displaying similar histopathological appearances, lesions of LCH may be best defined by clonality as well as cytokine expression and level of maturation. In future, such markers may be employed as prognostic indicators allowing individualised and targeted management.

BACKGROUND:Detection of B cell clonality is useful for assisting in the diagnosis of B cell lymphomas. Clonality assessment can be accomplished through evaluation of KAPPA and LAMBDA light chain expression. Currently, only slide based methods are available for the majority of patient biopsies and do not detect light chain protein or mRNA in many B-cell lymphomas. Herein we evaluated a new method, known as colorimetric in situ hybridization (CISH), with improved sensitivity and multiplexing capacity, for its usefulness in clonality detection in mature B cell malignancies.METHODS:The KAPPA and LAMBDA ISH was performed on a Ventana Benchmark XT utilizing two color chromogenetic detection. The probes comprised 2 haptenated riboprobes each approximately 500 base pairs long directed against the conserved regions of either KAPPA or LAMBDA mRNA. The dual colors consisted of silver deposition (black) for KAPPA light chain and a novel (pink) chromogen for LAMBDA light chain. Following optimization, CISH allowed visualization of mRNA in benign B cells in reactive tissues including germinal center, mantle zone, and post-germinal center cells. We then identified 79 cases of B cell lymphoma with formalin-fixed paraffin-embedded (FFPE) biopsies including: follicular (36 cases), mantle cell (6 cases), marginal zone (12 cases), lymphoplasmacytic (6 cases), small lymphocytic (4 cases), and diffuse large B cell (15 cases), which were selected on the basis of either prior flow cytometry or immunohistochemistry (IHC) results to serve as the predicate, "gold standard," comparator.RESULTS:39/79 (49.4%) cases were classified as KAPPA and 29/79 (36.7%) as LAMBDA light chain restricted / while 9/79 (11.3%) cases were classified as indeterminate. Of the 70 cases with KAPPA or LAMBDA light chain restricted CISH, 69/70 (98.6%) were concordant with the reference method, while 1/70 (1.4%) was discordant.CONCLUSIONS:Optimized CISH detected lower levels of mRNA than can be visualized with current slide based methods, making clonality assessment in FFPE biopsies possible for mature B cell neoplasms. In this preliminary study, CISH was highly accurate compared to flow cytometry or IHC. CISH offers the possibility of wider applicability of light chain ISH and is likely to become a useful diagnostic tool.Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1430491067123856

The brown macroalgae Fucus radicans is endemic to the Baltic Sea, but little is known about this newly described species. This thesis investigates the ecology and role of F. radicans within the species poor Baltic Sea ecosystem. The thallus of F. radicans had a more complex structure but was smaller than F. vesiculosus, the other important foundation species with which it grows in sympatry at several sites. The variability of the associated flora and fauna communities of these two Fucus species, however, was explained by the thallus size, not the complexity. Comparisons between the populations of F. radicans in the Bothnian Sea with those in Väinameri Sea on the Estonian coast, showed that the Estonian thalli were smaller, less complex and lacking the numerous adventitious branches which occur extensively in the Bothnian Sea populations. The distribution of F. radicans in Sweden is limited to the Bothnian Sea coast. The low salinity at the northern limit prevented successful fertilization, while increased salinity did not restrict F. radicans but improved its reproductive success. The southern distribution limit was instead shown to be negatively impacted by a combination of grazing and competition. The asexual reproduction through settling of detached fragments was favoured by high light levels and high temperature in laboratory conditions. Re-attachment occurred by basally formed rhizoids but settling also occurred through a calcium-rich substance, seemingly secreted by the fragment. Genetic spatial distribution of F. radicans showed a dominance of a few widespread clones both within and between sites with an intermingled rather than clustered pattern. The extensive female clone, common in most sites, is most likely old and several clonal lineages have derived from her.  Although more clearly expressed in the clonal populations, the macroscopic sexual dimorphism discovered appears to be a species specific trait in F. radicans. This thesis presents further insight in F. radicans role within the Baltic Sea ecosystem and its value as a study species for adaptation, clonality and speciation. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.</p>

As características fenotípicas e genotípicas de 203 isolados de Enterococcus spp. proveniente de diferentes amostras clínicas em dois hospitais localizados na cidade de Porto Alegre, Rio Grande do Sul, Brasil, foram estudadas. As espécies foram identificadas através de testes bioquímicos convencionais e pelo uso do sistema automatizado VITEK 2 (BioMérieux). As concentrações inibitórias mínimas (CIM) para aminoglicosídeos foram determinadas pelo método de diluição em ágar. O alto nível de resistência aos aminoglicosídeos (HLAR) e à ampicilina foi avaliado pelo mesmo método e adicionalmente pelo método de disco-difusão. A diversidade genética de amostras de Enterococcus faecalis com HLAR foi determinada através da digestão do DNA cromossômico com a enzima SmaI seguida de eletroforese em campo pulsado (PFGE). O E. faecalis foi a espécie mais prevalente (93,6%) seguido por E. faecium (4,4%). A resistência entre os isolados clínicos foi de 2,5% à ampicilina, 0,5% à vancomicina, 0,5% à teicoplanina, 33% ao cloranfenicol, 2% à nitrofurantoína, 62,1% à eritromicina, 64,5% à tetraciclina, 24,6% à rifampicina, 30% ao ciprofloxacino e 87,2% à quinupristina-dalfopristina. A prevalência de HLAR foi de 10,3%, sendo 23,6% para gentamicina e 37,4% para estreptomicina. A maioria das amostras sensíveis aos aminoglicosídeos pelo método de disco-difusão apresentaram CIM inferior a 125 μg/mL e 500μg/mL para gentamicina e estreptomicina, respectivamente. A prevalência de Enterococcus resistentes à vancomicina (ERV) foi muito baixa neste estudo. Um grupo clonal predominante foi encontrado entre amostras de E. faecalis com HLR-Ge/St. Os isolados incluídos no grupo clonal foram provenientes de ambos os hospitais, indicando uma disseminação intra e inter-hospitalar deste clone. / The phenotypic and genotypic characteristics of 203 Enterococcus spp isolates recovered from different clinical sources of two hospitals in Porto Alegre, Rio Grande do Sul, Brazil, were studied. The species were identified by conventional biochemical tests and the automated system VITEK 2 (BioMérieux). The minimal inhibitory concentrations (MIC) for aminoglycosides were evaluated by agar dilution method. The evaluation of high-level resistance to aminoglycosides (HLAR) and resistance to ampicillin were carried out by the same method as well as by the disc-diffusion method. The genetic diversity of HLAR E. faecalis was assessed by pulsed-field gel electrophoresis of cromossomal DNA after SmaI digestion. The E. faecalis was the most frequent specie (93.6%), followed by E. faecium (4.4%). The percentage of resistance among the clinical isolates was: 2.5% to ampicillin, 0.5% to vancomycin, 0.5% teicoplanin, 33% to chloramphenicol, 2% to nitrofurantoin, 66.1% to erythromycin, 66.5% to tetracycline, 24.6% to rifampicin, 30% to ciprofloxacin and 87.2% to quinupristin-dalfopristin. A total of 10.3% proved to be HLAR, with 23.6% resistant to gentamicin and 37.4% to streptomycin. Most of the aminoglycosides susceptible isolates by the disc-diffusion method presented MIC lower than 125 μg/mL and 500μg/mL for gentamicin e streptomycin, respectively. The prevalence of vancomycin resistance Enterococcus (VRE) was very low in this study. One predominant clonal group was found among E. faecalis exhibiting HLR-Ge/St. The isolates included in the clonal group were recovered from both hospitals, indicating both intrahospital and interhospital spread of this clone.

As características fenotípicas e genotípicas de 203 isolados de Enterococcus spp. proveniente de diferentes amostras clínicas em dois hospitais localizados na cidade de Porto Alegre, Rio Grande do Sul, Brasil, foram estudadas. As espécies foram identificadas através de testes bioquímicos convencionais e pelo uso do sistema automatizado VITEK 2 (BioMérieux). As concentrações inibitórias mínimas (CIM) para aminoglicosídeos foram determinadas pelo método de diluição em ágar. O alto nível de resistência aos aminoglicosídeos (HLAR) e à ampicilina foi avaliado pelo mesmo método e adicionalmente pelo método de disco-difusão. A diversidade genética de amostras de Enterococcus faecalis com HLAR foi determinada através da digestão do DNA cromossômico com a enzima SmaI seguida de eletroforese em campo pulsado (PFGE). O E. faecalis foi a espécie mais prevalente (93,6%) seguido por E. faecium (4,4%). A resistência entre os isolados clínicos foi de 2,5% à ampicilina, 0,5% à vancomicina, 0,5% à teicoplanina, 33% ao cloranfenicol, 2% à nitrofurantoína, 62,1% à eritromicina, 64,5% à tetraciclina, 24,6% à rifampicina, 30% ao ciprofloxacino e 87,2% à quinupristina-dalfopristina. A prevalência de HLAR foi de 10,3%, sendo 23,6% para gentamicina e 37,4% para estreptomicina. A maioria das amostras sensíveis aos aminoglicosídeos pelo método de disco-difusão apresentaram CIM inferior a 125 μg/mL e 500μg/mL para gentamicina e estreptomicina, respectivamente. A prevalência de Enterococcus resistentes à vancomicina (ERV) foi muito baixa neste estudo. Um grupo clonal predominante foi encontrado entre amostras de E. faecalis com HLR-Ge/St. Os isolados incluídos no grupo clonal foram provenientes de ambos os hospitais, indicando uma disseminação intra e inter-hospitalar deste clone. / The phenotypic and genotypic characteristics of 203 Enterococcus spp isolates recovered from different clinical sources of two hospitals in Porto Alegre, Rio Grande do Sul, Brazil, were studied. The species were identified by conventional biochemical tests and the automated system VITEK 2 (BioMérieux). The minimal inhibitory concentrations (MIC) for aminoglycosides were evaluated by agar dilution method. The evaluation of high-level resistance to aminoglycosides (HLAR) and resistance to ampicillin were carried out by the same method as well as by the disc-diffusion method. The genetic diversity of HLAR E. faecalis was assessed by pulsed-field gel electrophoresis of cromossomal DNA after SmaI digestion. The E. faecalis was the most frequent specie (93.6%), followed by E. faecium (4.4%). The percentage of resistance among the clinical isolates was: 2.5% to ampicillin, 0.5% to vancomycin, 0.5% teicoplanin, 33% to chloramphenicol, 2% to nitrofurantoin, 66.1% to erythromycin, 66.5% to tetracycline, 24.6% to rifampicin, 30% to ciprofloxacin and 87.2% to quinupristin-dalfopristin. A total of 10.3% proved to be HLAR, with 23.6% resistant to gentamicin and 37.4% to streptomycin. Most of the aminoglycosides susceptible isolates by the disc-diffusion method presented MIC lower than 125 μg/mL and 500μg/mL for gentamicin e streptomycin, respectively. The prevalence of vancomycin resistance Enterococcus (VRE) was very low in this study. One predominant clonal group was found among E. faecalis exhibiting HLR-Ge/St. The isolates included in the clonal group were recovered from both hospitals, indicating both intrahospital and interhospital spread of this clone.

As características fenotípicas e genotípicas de 203 isolados de Enterococcus spp. proveniente de diferentes amostras clínicas em dois hospitais localizados na cidade de Porto Alegre, Rio Grande do Sul, Brasil, foram estudadas. As espécies foram identificadas através de testes bioquímicos convencionais e pelo uso do sistema automatizado VITEK 2 (BioMérieux). As concentrações inibitórias mínimas (CIM) para aminoglicosídeos foram determinadas pelo método de diluição em ágar. O alto nível de resistência aos aminoglicosídeos (HLAR) e à ampicilina foi avaliado pelo mesmo método e adicionalmente pelo método de disco-difusão. A diversidade genética de amostras de Enterococcus faecalis com HLAR foi determinada através da digestão do DNA cromossômico com a enzima SmaI seguida de eletroforese em campo pulsado (PFGE). O E. faecalis foi a espécie mais prevalente (93,6%) seguido por E. faecium (4,4%). A resistência entre os isolados clínicos foi de 2,5% à ampicilina, 0,5% à vancomicina, 0,5% à teicoplanina, 33% ao cloranfenicol, 2% à nitrofurantoína, 62,1% à eritromicina, 64,5% à tetraciclina, 24,6% à rifampicina, 30% ao ciprofloxacino e 87,2% à quinupristina-dalfopristina. A prevalência de HLAR foi de 10,3%, sendo 23,6% para gentamicina e 37,4% para estreptomicina. A maioria das amostras sensíveis aos aminoglicosídeos pelo método de disco-difusão apresentaram CIM inferior a 125 μg/mL e 500μg/mL para gentamicina e estreptomicina, respectivamente. A prevalência de Enterococcus resistentes à vancomicina (ERV) foi muito baixa neste estudo. Um grupo clonal predominante foi encontrado entre amostras de E. faecalis com HLR-Ge/St. Os isolados incluídos no grupo clonal foram provenientes de ambos os hospitais, indicando uma disseminação intra e inter-hospitalar deste clone. / The phenotypic and genotypic characteristics of 203 Enterococcus spp isolates recovered from different clinical sources of two hospitals in Porto Alegre, Rio Grande do Sul, Brazil, were studied. The species were identified by conventional biochemical tests and the automated system VITEK 2 (BioMérieux). The minimal inhibitory concentrations (MIC) for aminoglycosides were evaluated by agar dilution method. The evaluation of high-level resistance to aminoglycosides (HLAR) and resistance to ampicillin were carried out by the same method as well as by the disc-diffusion method. The genetic diversity of HLAR E. faecalis was assessed by pulsed-field gel electrophoresis of cromossomal DNA after SmaI digestion. The E. faecalis was the most frequent specie (93.6%), followed by E. faecium (4.4%). The percentage of resistance among the clinical isolates was: 2.5% to ampicillin, 0.5% to vancomycin, 0.5% teicoplanin, 33% to chloramphenicol, 2% to nitrofurantoin, 66.1% to erythromycin, 66.5% to tetracycline, 24.6% to rifampicin, 30% to ciprofloxacin and 87.2% to quinupristin-dalfopristin. A total of 10.3% proved to be HLAR, with 23.6% resistant to gentamicin and 37.4% to streptomycin. Most of the aminoglycosides susceptible isolates by the disc-diffusion method presented MIC lower than 125 μg/mL and 500μg/mL for gentamicin e streptomycin, respectively. The prevalence of vancomycin resistance Enterococcus (VRE) was very low in this study. One predominant clonal group was found among E. faecalis exhibiting HLR-Ge/St. The isolates included in the clonal group were recovered from both hospitals, indicating both intrahospital and interhospital spread of this clone.

No description available.